class openfe.setup.atom_mapping.PersesAtomMapper(allow_ring_breaking: bool = True, preserve_chirality: bool = True, use_positions: bool = True, coordinate_tolerance: float = Quantity(value=0.25, unit=angstrom))#

Suggest atom mappings with the Perses atom mapper.

  • allow_ring_breaking (bool, optional) – this option checks if on only full cycles of the molecules shall be mapped, default: False

  • preserve_chirality (bool, optional) – if mappings must strictly preserve chirality, default: True

  • use_positions (bool, optional) – this option defines, if the

  • coordinate_tolerance (float, optional) – tolerance on how close coordinates need to be, such they can be mapped, default: 0.25*unit.angstrom

allow_ring_breaking: bool#
preserve_chirality: bool#
suggest_mappings(componentA: SmallMoleculeComponent, componentB: SmallMoleculeComponent) Iterable[LigandAtomMapping]#

Suggest LigandAtomMapping options for the input molecules.


an iterable over proposed mappings

Return type:


use_positions: bool#